Pysotope is an open-source package meant to processes raw data measured from the OSIBL GC-IRMS. Corrections are automatically calculated but the user must verify and confirm their application.
Note: pysotope was tested using jupyter lab and jupyter notebook. Compatibility with alternative python IDEs may require custom configuration.
- Drift (weighted means least squares)
- Linearity (log, exponential, or linear fit)
- Methanol derivitization - user is asked for methanol values
- PAME - calculates the isotopic composition of PAME, if run in the sequence (set argument pame=True)
- VSMOW - calculated using C18, C20, and C28 standards, tested on C24 standard.
- Uncertainty/error associted with each correction is automatically calculated and included in each data output.
- Compatible with hydrogen and carbon isotope measurements
- Modifiable standard isotopic values
- Due to non-linear linearity expression, a exponential or logarithmic curve is automatically fit to the linearity standards.
- Assign chain lengths using interactive plot (requires Jupyter Lab or Jupyter Notebook)
pip install pysotope- pame (default False) - if True, the package will automatically identify and correct PAME values in the sequence.
- user_linearity_conditions (default False) - if True, during linearity correction, user will be asked for a cutoff value under which samples with peak areas lower than the cutoff will be excluded from the analysis.
- alt_stds (default False) - if True, the user can modify the default standard values. These changes will be saved for the user, but will reset upon package update.
e.g.,
import pysotope
# Edit standard data
pysotope.standard_editor()
# Process IRMS data
pysotope.iso_process(pame=True, user_linearity_conditions = False)
# Assign chain lengths
%matplotlib widget
pysotope.assign_chain_lengths()- Run pysotope and provide the file path to the IRMS output data
- Answer questions
- Data output is split into mean of samples, individual samples, and standards in three .csv files
- Output log contains all user decisions, equations used for corrections, descriptive statistics, and time codes for user actions
- Figures are saved locally
Contributions to pysotope are welcome! If you encounter any issues or have suggestions for improvements, please open an issue or submit a pull request on the GitHub repository.
This project is licensed under the MIT License - see the LICENSE file for details.
For questions or inquiries, please contact:
- Author: Dr. Gerard Otiniano & Dr. Elizabeth Thomas
- Email: [email protected]